Did you try rebooting before removing the CMOS battery?
I have seen many systems with PS/2 keyboards that if you unplug it while the system is on and plug it back in it wont always work, i have also seen others where if its unplugged even for a second after you hit the power button it wont work until you reboot. PS/2 is a lot more finicky than USB is and has more issues with hot plugging.
I did try a a reboot, and I tried shutting down completely, plugging it back in and booting back up. I've also noticed that the media card reader is running much faster now since I cleared the CMOS. Its was very sluggish before. Very confusing.